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Persistent homology

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https://www.readbyqxmd.com/read/28327793/insights-into-cytochrome-bc1-complex-binding-mode-of-antimalarial-2-hydroxy-1-4-naphthoquinones-through-molecular-modelling
#1
Ana Carolina Rennó Sodero, Bárbara Abrahim-Vieira, Pedro Henrique Monteiro Torres, Pedro Geraldo Pascutti, Célia Rs Garcia, Vitor Francisco Ferreira, David Rodrigues da Rocha, Sabrina Baptista Ferreira, Floriano Paes Silva
BACKGROUND: Malaria persists as a major public health problem. Atovaquone is a drug that inhibits the respiratory chain of Plasmodium falciparum, but with serious limitations like known resistance, low bioavailability and high plasma protein binding. OBJECTIVES: The aim of this work was to perform molecular modelling studies of 2-hydroxy-1,4-naphthoquinones analogues of atovaquone on the Qo site of P. falciparum cytochrome bc1 complex (Pfbc1) to suggest structural modifications that could improve their antimalarial activity...
April 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28325102/building-up-and-breaking-down-mechanisms-controlling-recombination-during-replication
#2
Dana Branzei, Barnabas Szakal
The complete and faithful duplication of the genome is an essential prerequisite for proliferating cells to maintain genome integrity. This objective is greatly challenged by DNA damage encountered during replication, which causes fork stalling and in certain cases, fork breakage. DNA damage tolerance (DDT) pathways mitigate the effects on fork stability induced by replication fork stalling by mediating damage-bypass and replication fork restart. These DDT mechanisms, largely relying on homologous recombination (HR) and specialized polymerases, can however contribute to genome rearrangements and mutagenesis...
March 22, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28319048/amino-acid-insensitive-mtorc1-regulation-enables-nutritional-stress-resilience-in-hematopoietic-stem-cells
#3
Demetrios Kalaitzidis, Dongjun Lee, Alejo Efeyan, Youmna Kfoury, Naema Nayyar, David B Sykes, Francois E Mercier, Ani Papazian, Ninib Baryawno, Gabriel D Victora, Donna Neuberg, David M Sabatini, David T Scadden
The mTOR pathway is a critical determinant of cell persistence and growth wherein mTOR complex 1 (mTORC1) mediates a balance between growth factor stimuli and nutrient availability. Amino acids or glucose facilitates mTORC1 activation by inducing RagA GTPase recruitment of mTORC1 to the lysosomal outer surface, enabling activation of mTOR by the Ras homolog Rheb. Thereby, RagA alters mTORC1-driven growth in times of nutrient abundance or scarcity. Here, we have evaluated differential nutrient-sensing dependence through RagA and mTORC1 in hematopoietic progenitors, which dynamically drive mature cell production, and hematopoietic stem cells (HSC), which provide a quiescent cellular reserve...
March 20, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28314191/robust-detection-and-segmentation-of-cell-nuclei-in-biomedical-images-based-on-a-computational-topology-framework
#4
Rodrigo Rojas-Moraleda, Wei Xiong, Niels Halama, Katja Breitkopf-Heinlein, Steven Dooley, Luis Salinas, Dieter W Heermann, Nektarios A Valous
The segmentation of cell nuclei is an important step towards the automated analysis of histological images. The presence of a large number of nuclei in whole-slide images necessitates methods that are computationally tractable in addition to being effective. In this work, a method is developed for the robust segmentation of cell nuclei in histological images based on the principles of persistent homology. More specifically, an abstract simplicial homology approach for image segmentation is established. Essentially, the approach deals with the persistence of disconnected sets in the image, thus identifying salient regions that express patterns of persistence...
March 6, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28284606/use-of-signature-tagged-mutagenesis-to-identify-genes-associated-with-colonization-of-sheep-by-e-coli-o157-h7
#5
Nancy A Cornick, Josh Pitzer, Amy F Helgerson, Melissa L Madsen, Kathy T Kurth, Qianjun Xiao, F Chris Minion
Outbreaks of Escherichia coli O157:H7 in the United States due to contaminated foods are a public health issue and a continuing problem. The major reservoir for these organisms is the gastrointestinal tract of ruminants where they are a member of the resident microbiota. Several factors that contribute to the colonization of cattle have been identified, but a systematic screen of genes that might contribute to the colonization and persistence phenotype in mature ruminants has not been reported. Using a sheep model of persistence, signature tagged mutagenesis (STM) was used to screen 1326 mutants for a persistence-negative phenotype of E...
March 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28278024/functional-elucidation-of-hypothetical-proteins-for-their-indispensable-roles-towards-drug-designing-targets-from-helicobacter-pylori-strain-hpag1
#6
Gagandeep Singh, Vikram Singh
Helicobacter pylori is a flagellated and slow growing gram-negative bacterium that persistently infects about half of the entire world population. In present study, we examined the proteome of Helicobacter pylori strain HPAG1 for identification of key uncharacterized proteins towards their novel regulatory functions. The complete proteome of this strain consists of 1539 proteins, out of which 520 proteins are annotated as hypothetical. Based on the functional motifs in their primary sequences, we were able to classify 254 of these hypothetical proteins into 6 functional categories...
March 3, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28272393/experimental-vaccine-induces-th1-driven-immune-responses-and-resistance-to-neisseria-gonorrhoeae-infection-in-a-murine-model
#7
Y Liu, L A Hammer, W Liu, M M Hobbs, R A Zielke, A E Sikora, A E Jerse, N K Egilmez, M W Russell
Female mice were immunized intravaginally with gonococcal outer membrane vesicles (OMVs) plus microencapsulated interleukin-12 (IL-12), and challenged using an established model of genital infection with Neisseria gonorrhoeae. Whereas sham-immunized and control animals cleared the infection in 10-13 days, those immunized with OMV plus IL-12 cleared infection with homologous gonococcal strains in 6-9 days. Significant protection was also seen after challenge with antigenically distinct strains of N. gonorrhoeae, and protective anamnestic immunity persisted for at least 6 months after immunization...
March 8, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/28261862/a-putative-tir-domain-protein-from-helicobacter-pylori-is-dimeric-in-solution-and-interacts-with-human-tlr-adaptor-myeloid-differentiation-primary-response-88
#8
Burcu Kaplan Türköz
Helicobacter pylori is an important human pathogen capable of causing persistent infection with minimal immune response. The first line of defense during H. pylori infection is through gastric epithelial cells that present Toll like receptors (TLR), a family of bacterial proteins which share homology with the Toll/IL1 receptor (TIR) domain. Bacterial TIR proteins (BTP) mimic human TIR domain proteins and act on MyD88 signaling pathways to suppress TLR signaling. H. pylori might also produce a similar protein...
March 6, 2017: Microbiology and Immunology
https://www.readbyqxmd.com/read/28257444/mechanisms-of-fast-and-stringent-search-in-homologous-pairing-of-double-stranded-dna
#9
Amir Bitran, Wei-Yin Chiang, Erel Levine, Mara Prentiss
Self-organization in the cell relies on the rapid and specific binding of molecules to their cognate targets. Correct bindings must be stable enough to promote the desired function even in the crowded and fluctuating cellular environment. In systems with many nearly matched targets, rapid and stringent formation of stable products is challenging. Mechanisms that overcome this challenge have been previously proposed, including separating the process into multiple stages; however, how particular in vivo systems overcome the challenge remains unclear...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28245427/microbe-microbe-and-host-microbe-interactions-drive-microbiome-dysbiosis-and-inflammatory-processes
#10
Amy D Proal, Inge A Lindseth, Trevor G Marshall
An extensive microbiome comprised of bacteria, viruses, bacteriophages, and fungi is now understood to persist in nearly every human body site, including tissue and blood. The genomes of these microbes continually interact with the human genome in order to regulate host metabolism. Many components of this microbiome are capable of both commensal and pathogenic activity. They are additionally able to persist in both 'acute' and chronic forms. Inflammatory conditions historically studied separately (autoimmune, neurological and malignant) are now repeatedly tied to a common trend: imbalance or dysbiosis of these microbial ecosystems...
January 2017: Discovery Medicine
https://www.readbyqxmd.com/read/28229982/circulating-free-dna-mutation-associated-with-response-of-targeted-therapy-in-human-epidermal-growth-factor-receptor-2-positive-metastatic-breast-cancer
#11
Qing Ye, Fan Qi, Li Bian, Shao-Hua Zhang, Tao Wang, Ze-Fei Jiang
BACKGROUND: The addition of anti-human epidermal growth factor receptor 2 (HER2)-targeted drugs, such as trastuzumab, lapatinib, and trastuzumab emtansine (T-DM1), to chemotherapy significantly improved prognosis of HER2-positive breast cancer patients. However, it was confused that metastatic patients vary in the response of targeted drug. Therefore, methods of accurately predicting drug response were really needed. To overcome the spatial and temporal limitations of biopsies, we aimed to develop a more sensitive and less invasive method of detecting mutations associated with anti-HER2 therapeutic response through circulating-free DNA (cfDNA)...
March 5, 2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28214649/evaluation-of-dioxins-and-dioxin-like-compounds-from-a-cement-plant-using-carbide-slag-from-chlor-alkali-industry-as-the-major-raw-material
#12
Yuyang Zhao, Jiayu Zhan, Guorui Liu, Minghui Zheng, Rong Jin, Lili Yang, Liwei Hao, Xiaolin Wu, Xian Zhang, Pu Wang
Carbide slag produced from chlor-alkali industry contains high amounts of calcium compounds and can potentially be used as raw material for cement production; however, it contains large amounts of chlorine so it is essential to evaluate the emissions of chlorinated organic pollutants, including polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), polychlorinated biphenyls (PCBs), and polychlorinated naphthalenes (PCNs). A field study of the emission profiles of these pollutants in a cement plant using such slag was performed...
February 14, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28208329/persistent-homology-analysis-of-craze-formation
#13
Takashi Ichinomiya, Ippei Obayashi, Yasuaki Hiraoka
We apply a persistent homology analysis to investigate the behavior of nanovoids during the crazing process of glassy polymers. We carry out a coarse-grained molecular dynamics simulation of the uniaxial deformation of an amorphous polymer and analyze the results with persistent homology. Persistent homology reveals the void coalescence during craze formation, and the results suggest that the yielding process is regarded as the percolation of nanovoids created by deformation.
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28192542/functional-diversity-of-secreted-cestode-kunitz-proteins-inhibition-of-serine-peptidases-and-blockade-of-cation-channels
#14
Martín Fló, Mariana Margenat, Leonardo Pellizza, Martín Graña, Rosario Durán, Adriana Báez, Emilio Salceda, Enrique Soto, Beatriz Alvarez, Cecilia Fernández
We previously reported a multigene family of monodomain Kunitz proteins from Echinococcus granulosus (EgKU-1-EgKU-8), and provided evidence that some EgKUs are secreted by larval worms to the host interface. In addition, functional studies and homology modeling suggested that, similar to monodomain Kunitz families present in animal venoms, the E. granulosus family could include peptidase inhibitors as well as channel blockers. Using enzyme kinetics and whole-cell patch-clamp, we now demonstrate that the EgKUs are indeed functionally diverse...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28192223/emergence-of-multi-drug-resistance-among-soil-bacteria-exposing-to-insecticides
#15
Kirubakaran Rangasamy, Murugan Athiappan, Natarajan Devarajan, Javid A Parray
Impacts of pesticide exposure on the soil microbial flora and cross resistance to antibiotics have not been well documented. Development of antibiotic resistance is a common issue among soil bacteria which are exposing to pesticides continuously at sub-lethal concentration. The present study was focused to evaluate the correlation between pesticide exposures and evolution of multi drug resistance among isolates collected from soil applied with insecticides. Twenty five insecticide (Monochrotophos) degrading bacteria were isolated from contaminated agricultural soil...
February 10, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28184004/ets-proto-oncogene-1-transcriptionally-up-regulates-the-cholangiocyte-senescence-associated-protein-cyclin-dependent-kinase-inhibitor-2a
#16
Steven P O'Hara, Patrick L Splinter, Christy E Trussoni, Maria J Lorenzo Pisarello, Lorena Loarca, Noah S Splinter, Bryce F Schutte, Nicholas F LaRusso
Primary sclerosing cholangitis (PSC) is a chronic, fibro-inflammatory cholangiopathy (disease of the bile ducts) of unknown pathogenesis. We reported that cholangiocyte senescence features prominently in PSC and neuroblastoma RAS viral oncogene homolog (NRAS) is activated in PSC cholangiocytes. Additionally, persistent microbial insult (e.g., lipopolysaccharides [LPS]) induces Cyclin Dependent Kinase Inhibitor 2A (CDKN2A/p16INK4a) expression and senescence in cultured cholangiocytes in an NRAS-dependent manner...
February 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28169281/gating-of-memory-encoding-of-time-delayed-cross-frequency-meg-networks-revealed-by-graph-filtration-based-on-persistent-homology
#17
Jarang Hahm, Hyekyoung Lee, Hyojin Park, Eunjoo Kang, Yu Kyeong Kim, Chun Kee Chung, Hyejin Kang, Dong Soo Lee
To explain gating of memory encoding, magnetoencephalography (MEG) was analyzed over multi-regional network of negative correlations between alpha band power during cue (cue-alpha) and gamma band power during item presentation (item-gamma) in Remember (R) and No-remember (NR) condition. Persistent homology with graph filtration on alpha-gamma correlation disclosed topological invariants to explain memory gating. Instruction compliance (R-hits minus NR-hits) was significantly related to negative coupling between the left superior occipital (cue-alpha) and the left dorsolateral superior frontal gyri (item-gamma) on permutation test, where the coupling was stronger in R than NR...
February 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28166814/closely-related-borrelia-burgdorferi-sensu-stricto-strains-exhibit-similar-fitness-in-single-infections-and-asymmetric-competition-in-multiple-infections
#18
Evelyn C Rynkiewicz, Julia Brown, Danielle M Tufts, Ching-I Huang, Helge Kampen, Stephen J Bent, Durland Fish, Maria A Diuk-Wasser
BACKGROUND: Wild hosts are commonly co-infected with complex, genetically diverse, pathogen communities. Competition is expected between genetically or ecologically similar pathogen strains which may influence patterns of coexistence. However, there is little data on how specific strains of these diverse pathogen species interact within the host and how this impacts pathogen persistence in nature. Ticks are the most common disease vector in temperate regions with Borrelia burgdorferi, the causative agent of Lyme disease, being the most common vector-borne pathogen in North America...
February 6, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28164792/characterization-and-function-of-mycobacterium-tuberculosis-h37rv-lipase-rv1076-lipu
#19
Chunyan Li, Qiming Li, Yuan Zhang, Zhen Gong, Sai Ren, Ping Li, Jianping Xie
Lipids and lipases/esterases are essential for Mycobacterium tuberculosis (Mtb) survival and persistence, even virulence. Mycobacterium tuberculosis H37Rv Rv1076 (LipU), a member of lipase family, is homologous to the human Hormone Sensitive Lipase (HSL) based on the presence of conserved motif 'GXSXG'. To define the enzymatic characteristics of rv1076, the gene was cloned, and expressed in Escherichia coli. The protein was purified for enzymatic characterization. LipU showed high specific activity for the hydrolysis of short carbon chain substrates with optimal activity at 40°C/pH 8...
March 2017: Microbiological Research
https://www.readbyqxmd.com/read/28161890/homology-guided-mutational-analysis-reveals-the-functional-requirements-for-antinociceptive-specificity-of-collapsin-response-mediator-protein-2-derived-peptides
#20
Aubin Moutal, Wennan Li, Yue Wang, Weina Ju, Shizhen Luo, Song Cai, Liberty François-Moutal, Samantha Perez-Miller, Jackie Hu, Erik T Dustrude, Todd W Vanderah, Vijay Gokhale, May Khanna, Rajesh Khanna
BACKGROUND AND PURPOSE: N-type voltage-gated calcium (Cav 2.2) channels are critical determinants of increased neuronal excitability and neurotransmission accompanying persistent neuropathic pain. Although Cav 2.2 channel antagonists are recommended as first-line treatment for neuropathic pain, calcium-current blocking gabapentinoids inadequately alleviate chronic pain symptoms and often exhibit numerous side effects. Collapsin response mediator protein 2 (CRMP2) targets Cav 2.2 channels to the sensory neuron membrane and allosterically modulates their function...
February 5, 2017: British Journal of Pharmacology
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